For the ships, once I've found the models (I've only got the Venator currently), I'll use either a 3D printer or shapeways.com to get them 3d printed.
For Order 66, I think there will be a Darkness Marker on a track of 10-16 spaces, and the Sith will perform missions to attempt to sway the force towards the dark side. At the same time, the Jedi will be attempting to stop that as well as find out who the Dark Lord is. When the Darkness reaches the end of the track, the Sith will win, as the war has gone on long enough for the citizens of the galaxy to believe that the Jedi are traitors, and so Order 66 is executed.

I had a look at the cards, my favourite two one are:
EWOKS! But no ewok units (says "play if at least 9 systems have rebel loyalty")
and Promotion. A whole free leader! Oh yiss!
The jabba-only action card:
Cirrut/Jyn card: (why jyn?)
Decisive victory (objective) (has the Ghost [from rebels] pictured)
as an aside, Jabba has no combat values.
Finally, when someone finds out what the vader symbol on some of the missions does, tell me!

Oh yeah, the Army cards would also have 2 Jedi pictured, and you would be forced to place one in the attacked system. Continuing the above example, the army card might have Anakin and Ahsoka pictured, and you could choose to send either Ahsoka or Anakin, and use his/her combat values during that battle.
P.S. May the Fourth be with you!

Think of your least favourite republic leader I created. I removed Jar-Jar because I preferred the other leader.
I'm actually going to go with @hstruman's idea of making the players play as Sith or Jedi instead of CIS or Republic. I'm going to simulate the Republic & CIS moving with army cards, which will say something like "Move 1 Venator, 2 Gunships, and 3 Clone troopers to Cato Nemoidia", as an example.
I'd love more suggestions though!

I just realised I've missed the build numbers on the board, but since I'm using @hstruman 's idea (look above) of playing as either Jedi or Sith instead of Republic or CIS, I won't need that, as building will be automated.

You know, it might actually be better to seperate the Jedi/Sith from the fight like you're saying, and kind of automate the Republic/CIS.
This would also actually be more accurate, as the Jedi could essentially do anything they wanted, but the Republic was severely hampered by the Senate. The same happened with the Sith and the CIS, only to a lesser extent.
I think I'd still keep the dark lord secret, so that the Jedi do not know who he/she(Darth Padme?) is.
I especially like the part where the Sith causes Republic & CIS forces to fight, I'll have to give a reason for them to do so. Maybe battles increase the darkness?
Thanks,
IrishCyborg

I've just finished the board for the game, I made it completely from scratch, the images are mostly taken from Wookiepedia.
Note that both Coruscant and Geonosis are always loyal to their corresponding sides.
And the other possible starting positions are shown below.
You can read more about this game on my website.
P.S. I explain these --> on my website.